AP Biology Unit 6 - Gene Expression and Regulation

nucleic acids

• basis for heredity for all life in earth

eukaryotic DNA

• structured in multiple linear chromosomes contained w/in nucleus

• each chromosome contains unique set of genes that carry information for making RNA and in turn proteins

• additional genetic info can be housed outside of chromosome

prokaryotic DNA

• structured in a single circular chromosome

• additional genetic info can be housed outside of chromosome

extra-chromosomal DNA

• additional genetic info can be housed outside of chromosome

• ex. plasmids, mitochondrial/chloroplastic DNA

plasmids

• both prokaryotes and eukaryotes can have small, circular, double-stranded DNA molecules (extra-chromosomal)

semiconservative replication

• the process by which DNA is copied

• one strand of DNA serves as a template for the second strand to form

• some enzymes and RNA are involved in this process

helicase

• enzyme that separates double strands into single strands

• allows replication machinery access to single strands of DNA

replication fork

• point where DNA splits into 2 strands

topoisomerase

• works just in front of replication fork to keep double stranded DNA from supercoiling

• breaks phosphate backbone, allowing for unwinding and resealing DNA

DNA polymerase III

• synthesizes new DNA by adding new nucleotides to the 3’ end of DNA

• because of this, DNA is always synthesized in 5’ to 3’ direction

• DNA polymerases are capable of proofreading their work so they are able to correct any mistakes made in replication

RNA primers

• required for DNA polymerases do not initiate synthesis of a single strand of DNA

• short strands of nucleotides

• DNA polymerase acts by adding new nucleotides at the end of the RNA primers

• eventually replaced by DNA polymerase I

DNA polymerase I

• eventually replaces the RNA primers

leading strand

• the strand of DNA that is continuously repliacted on

lagging strand

• “anti-parallel strand”

• DNA is replicated in short segments called Okazaki fragments

• RNA primers are attached to sections of DNA strands and DNA polymerase III adds nucleotides in the 5’ to 3’ direction btwn primers

• DNA ligase seals gaps btwn double stranded fragments on lagging strand

okazagi fragments

• DNA is replicated in short segments called Okazaki fragments on the lagging strand

DNA ligase

• seals gaps btwn double stranded fragments on lagging strand

origin of replication

• circular DNA in most prokaryotes have one specific sequence of DNA that signals where replication begins

  • this sequence is called the origin of replication

• when DNA replicates, replication bubble forms w/ 2 replication forks @ each end

• bubble grows until you have 2 copies of DNA

• in eukaryotes : each chromosome has many origins of replication

  • due to the way lagging strand is formed, some DNA is lost in each round of replication at telomeres

telomeres

• ends of linear chromosomes

genes

• stretches of DNA that encode blueprints to make RNA and, in turn, proteins

making proteins 1 : transcription

• mRNA is formed

• 2 DNA strands in helix unzip to allow RNA polymerase to make a complementary copy of the gene (mRNA)

mRNA

• messenger RNA

• made in 5’ to 3’ direction by reading DNA strand in 3’ to 5’ direction

RNA polymerase

• synthesizes RNA by following a strand of DNA

pre-mRNA

• newly transcribed mRNA

• not yet ready for export from nucleus and translation to protein

posttransational modifications

• for mRNA to mature

• addition of 5’ GTP cap

  • important for targeting mRNA for nuclear export, preventing degredation, promoting translation

  • poly(A) tail is also added to 3’ end of mRNA

poly(A) tail

• string of adenosines that are important for nuclear export, protection from degredation, and translation

introns

• some parts of sequence that do not translate into proteins

• must be removed throguh splicing

RNA splicing

• process where newly-made precusor messenger RNA transcript is transformed into a mature messenger RNA

• removes all introns and splices exons back together

exons

• parts of the gene that encodes mature mRNA

• selectively included or excluded, resulting in several different sequences of proteins from the same gene in an organism

alternative splicing

• selectively included or excluded, resulting in several different sequences of proteins from the same gene in an organism

making proteins 2 : translation

• shuttled out of nucleus to cytoplasm for next step

• proteins are made

• mRNA enters ribosome where tRNA translates message to make proteins

• tRNA recognizes mRNA sequences and translates them to amino acid sequences

• bulk of ribosomes are also made of rRNA and proteins

• ribosomes bring mRNA and complimentary tRNAs together so protein forms

• eukaryotes : ribosomes are found both in cytoplasm and on rough endoplasmic reticulum; translation can occur @ either of these sites

• prokaryotes : translation occurs in cytoplasm

tRNA

• transfer RNA

• translate message to make proteins

• link between mRNA and chain of amino acids

rRNA

• ribosomal RNA

• makes up ribosomes

• exported to cytoplasm ot help translate mRNA information into protein

translation 1 : initiation

• start codon signals start of translation

• RNA-amino acid code is universal for all life on Earth

• same sequence of codons encodes same amino acids for any form of life, providing evidence of a common ancestor

start codon

• mRNA sequence that signals start of translation

codons

• groups of three base pairs, the sequence of which encodes either a specific amino acid or start of stop sequence

translation 2 : elongation

• tRNA read mRNA codon through RNA interactions

• signals attached amino acid to be transferred to growing protein chain called polypeptide chain

• mRNA continues to elongate until it reaches stop codon

stop codon

• signals termination of translation

translation 3 : termination

• translation is stopped

• newly formed protein is released

prokaryote translation

• no nucleus : transcription and translation occur simultaneously

• have some forms of posttranslational modifications but different than those of eukaryotes

• no known introns, no alternative splicing

retroviruses

• viruses made of RNA

• genetic info from retroviruses is first reverse-transcribed into DNA through reverse transcriptase

• DNA integrates into the genome of the infected cell through integrate

• once integrated, virus takes advantage of transcription and translation machinery of cell to replicate new viral progeny

reverse transcriptase

• enzyme

• takes single stranded viral RNA molecule and transcribes it into a double stranded DNA

integrase

• enzyme

• helps viral DNA to enter into genome of affected cell

transcription factors

• proteins that regulate transcription of subsets of genes

• expressed during organism development to help determine which subsets of genes are expressed and what type of cell is ultimately formed

regulatory sequences

• stretches of DNA that control transcription

• help modulate expression of genes

• transcription factors and other gene regulatory proteins identify specific regulatory sequences and use those as a guide to direct which genes are expressed and how much protein is made

promoters

• sequences where RNA polymerase and transcription factors bind to initiate transcription

enhancers

• regulatory sequences where proteins bind to increase the likelihood of transcription occuring

• negative regulatory molecules also exist that decrease transcription

• ex. silencers

silencers

• DNA sequences that bind proteins called repressors and block RNA polymerase from binding

operons (called operons in prokaryotes)

• groups of genes regulated together as a group by a single promotor generating a single mRNA

• ex. lac operon - contains all proteins for a cell to metabolize lactose

eukaryotic operons

• gene exp coordinated through expression of transcription factors that regulate many genes in different locations that specify a cell type

epigenetics

• modifications in gene expression through factors other than alterations to DNA sequence

• ex. methylation of DNA or alterations to histones that DNA wraps around in cells

• changes can enhance or reduce gene exp.

mutations

• alterations in genes or the produces that they make

• can be negative, neutral, or positive based on the effect they have on the organism

• emergence of mutations that affect phenotypes —> basis for genetic diversity of a species

• can be caused by errors in DNA replication or repair, external factors (radiation, exposure to mutagenic chemicals), errors in mitosis or meiosis can change chromosome number

  • whether its a negative or positive effect depends on the environment

missene mutations

• changes in one single base pair of DNA, causing an amino acid to change from one type to another

nonsense mutations

• result of a single base pair change that causes a premature stop codon to appear and shortened protein to be produced

insertion mutations

• caused by the insertion of a short piece of DNA into a genes

deletion mutations

• occur when one or many base pairs of DNA are deleted

• can affect single gene or many genes

duplication mutations

• result of a bit of DNA being copied one or many times

frameshift mutations

• insertion or deletion of base pairs causes codon frame of a gene to shift so part of the protein downstram of the mutation translates to different amino acids

• happens whenever there is an insertion or deletion in an exon that is not a multiple of 3 base pairs

errors in meiosis or mitosis

• cause changes in chromosome number

• in reproduction, chromosomal mutations can cause new phenotypes to emergy, like sterily

• can result in developmental limitations, as is the case for individuals affected by Down syndrome

mechanisms for sharing DNA

• allow for the enhanced survival and reproduction of a species

• ex. horizontal transfer of DNA in form of plasmids, either throguh uptake of naked DNA or through cell-to-cell transmission

  • uptake of viral DNA —> alters DNA sequence

electrophoresis

• method used to separate molecules by size na dcharge

• used to separate DNA, RNA, or protein fragments to help scientists identify what molecules are present

polymerase chain reaction (PCR)

• used to amplify a single DNA fragment into many identical fragments

• by selectively amplifying a sequence of DNA, scientists are more easily able to identify it through electrophoresis, sequence it, or transfect it into other cells

bacterial transformation

• takes advantage of horizontal gene transfer to introduce new DNA to bacteria

• can be used to produce a protein of interest in large amounts

• methods have also been established to allow gene transfer in eukaryotes, including humans

horizontal gene transfer

• movement of genetic information across normal mating barriers, between more or less distantly related organisms

DNA sequencing

• determines genetic sequence of nucleotides in DNA

• can be small scale or whole genome sequencing that determines entire genetic code of an organism